galaxy-europe

Data intensive science for everyone.

https://github.com/marie59/galaxy-europe

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Data intensive science for everyone.

Basic Info

Host: GitHub
Owner: Marie59
License: other
Language: Python
Default Branch: release_23.1_europe
Homepage: https://galaxyproject.org/
Size: 646 MB

Statistics

Stars: 0
Watchers: 0
Forks: 0
Open Issues: 0
Releases: 0

Created over 2 years ago · Last pushed 9 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Security

README.rst

.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
   :alt: Galaxy Logo

The latest information about Galaxy can be found on the `Galaxy Community Hub `__.

Community support is available at `Galaxy Help `__.

.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
    :target: https://gitter.im/galaxyproject/Lobby
    :alt: Chat on gitter

.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
    :target: https://webchat.freenode.net/?channels=galaxyproject
    :alt: Chat on irc

.. image:: https://img.shields.io/badge/release-documentation-blue.svg
    :target: https://docs.galaxyproject.org/en/master/
    :alt: Release Documentation

.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
    :target: https://travis-ci.org/galaxyproject/galaxy
    :alt: Inspect the test results

Galaxy Quickstart
=================

Galaxy requires Python 3.7 . To check your Python version, run:

.. code:: console

    $ python -V
    Python 3.7.6

Start Galaxy:

.. code:: console

    $ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080

For more installation details please see: https://getgalaxy.org/

Documentation is available at: https://docs.galaxyproject.org/

Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/

Tools
=====

Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial `__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.

Issues and Galaxy Development
=============================

Please see `CONTRIBUTING.md `_ .

Owner

Name: Marie Jossé
Login: Marie59
Kind: user

Repositories: 5
Profile: https://github.com/Marie59

marie.josse@mnhn.fr

Citation (CITATION)

If you use or extend Galaxy in your published work, please cite this
publication:

- The Galaxy Community. "The Galaxy platform for accessible, reproducible and collaborative
  biomedical analyses: 2022 update"
  Nucleic Acids Res. (2022) 50(W1):W345-W351 doi:10.1093/nar/gkac247

BibTeX format:

@article{10.1093/nar/gkac247,
  title = {The {Galaxy} platform for accessible, reproducible and collaborative biomedical analyses: 2022 update},
  author = {The Galaxy Community},
  journal = {Nucleic Acids Res.},
  doi = {10.1093/nar/gkac247},
  volume = {50},
  number = {W1},
  pages = {W345-W351},
  year = {2022},
  url = {https://doi.org/10.1093/nar/gkac247},
  publisher = {Oxford University Press}
}


More publications
-----------------

To cite specific Galaxy components/features or other Galaxy project
publications, see

https://galaxyproject.org/citing-galaxy

GitHub Events

Total

Delete event: 1
Push event: 22
Create event: 3

Last Year

Delete event: 1
Push event: 22
Create event: 3

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Dependencies

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client/yarn.lock npm

1586 dependencies

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config/plugins/visualizations/nvd3/nvd3_bar/package.json npm

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config/plugins/visualizations/openlayers/package.json npm

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config/plugins/visualizations/scatterplot/package.json npm

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config/plugins/visualizations/ts_visjs/package.json npm

vis ^4.21.0

config/plugins/visualizations/venn/package.json npm

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config/plugins/webhooks/demo/tour_generator/package.json npm

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config/plugins/welcome_page/new_user/package.json npm

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lib/galaxy/web/proxy/js/package.json npm

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package.json npm

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lib/galaxy/dependencies/conditional-requirements.txt pypi

azure-storage ==0.32.0
boto3 *
chronos-python ==1.2.1
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drmaa *
fluent-logger *
fs-basespace *
fs-gcsfs *
fs-onedatafs *
fs.anvilfs *
fs.dropboxfs *
fs.googledrivefs *
fs.sshfs *
fs.webdavfs >=0.4.2
galaxycloudrunner *
google-cloud-storage >=2.8.0
hvac *
influxdb *
kamaki *
ldap3 ==2.9.1
mysqlclient *
pbs_python *
pkce *
psycopg2-binary ==2.9.5
pygithub *
pykube ==0.15.0
python-gitlab >=2.10.0
python-irodsclient ==1.1.3
python-ldap ==3.4.0
python-pam *
sentry-sdk *
statsd *
tensorflow *
total-perspective-vortex >=2.3.2,<3
watchdog *
weasyprint *

lib/galaxy/dependencies/dev-requirements.txt pypi

aiohttp ==3.8.4 development
aiosignal ==1.3.1 development
alabaster ==0.7.13 development
amqp ==5.1.1 development
anyio ==3.7.0 development
ase ==3.22.1 development
async-generator ==1.10 development
async-timeout ==4.0.2 development
asynctest ==0.13.0 development
attrs ==23.1.0 development
axe-selenium-python ==2.1.6 development
babel ==2.12.1 development
billiard ==3.6.4.0 development
black ==23.3.0 development
bleach ==6.0.0 development
build ==0.10.0 development
cachecontrol ==0.13.1 development
cached-property ==1.5.2 development
celery ==5.2.7 development
certifi ==2023.5.7 development
cffi ==1.15.1 development
charset-normalizer ==3.1.0 development
click ==8.1.3 development
click-didyoumean ==0.3.0 development
click-plugins ==1.1.1 development
click-repl ==0.3.0 development
codespell ==2.2.5 development
colorama ==0.4.6 development
coverage ==7.2.7 development
cryptography ==41.0.1 development
cwltest ==2.3.20230527113600 development
cycler ==0.11.0 development
darker ==1.7.1 development
defusedxml ==0.7.1 development
deprecated ==1.2.14 development
docutils ==0.18.1 development
exceptiongroup ==1.1.1 development
filelock ==3.12.2 development
fluent-logger ==0.10.0 development
fonttools ==4.38.0 development
frozenlist ==1.3.3 development
future ==0.18.3 development
galaxy-release-util ==0.1.2 development
h11 ==0.14.0 development
httpcore ==0.17.2 development
httpx ==0.24.1 development
idna ==3.4 development
imagesize ==1.4.1 development
importlib-metadata ==4.13.0 development
importlib-resources ==5.12.0 development
iniconfig ==2.0.0 development
isodate ==0.6.1 development
isort ==5.11.5 development
jaraco-classes ==3.2.3 development
jeepney ==0.8.0 development
jinja2 ==3.1.2 development
junit-xml ==1.9 development
keyring ==23.13.1 development
kiwisolver ==1.4.4 development
kombu ==5.2.4 development
lxml ==4.9.2 development
markdown-it-py ==2.2.0 development
markdown-it-reporter ==0.0.2 development
markupsafe ==2.1.3 development
matplotlib ==3.5.3 development
matplotlib ==3.7.1 development
mdit-py-plugins ==0.3.5 development
mdurl ==0.1.2 development
mirakuru ==2.5.1 development
mistune ==2.0.5 development
more-itertools ==9.1.0 development
msgpack ==1.0.5 development
multidict ==6.0.4 development
mypy-extensions ==1.0.0 development
myst-parser ==1.0.0 development
numpy ==1.21.6 development
numpy ==1.24.3 development
numpy ==1.25.0 development
outcome ==1.2.0 development
packaging ==23.1 development
pathspec ==0.11.1 development
pillow ==9.5.0 development
pkce ==1.0.3 development
pkginfo ==1.9.6 development
platformdirs ==3.6.0 development
pluggy ==1.0.0 development
port-for ==0.7.0 development
prettytable ==3.7.0 development
prompt-toolkit ==3.0.38 development
psutil ==5.9.5 development
py ==1.11.0 development
pycparser ==2.21 development
pygithub ==1.58.2 development
pygments ==2.15.1 development
pyjwt ==2.7.0 development
pynacl ==1.5.0 development
pyparsing ==3.0.9 development
pyproject-hooks ==1.0.0 development
pysocks ==1.7.1 development
pytest ==7.3.2 development
pytest-asyncio ==0.21.0 development
pytest-celery ==0.0.0 development
pytest-cov ==4.1.0 development
pytest-html ==3.2.0 development
pytest-httpserver ==1.0.6 development
pytest-json-report ==1.5.0 development
pytest-metadata ==3.0.0 development
pytest-mock ==3.11.1 development
pytest-postgresql ==4.1.1 development
pytest-shard ==0.1.2 development
python-dateutil ==2.8.2 development
python-irodsclient ==1.1.8 development
pytz ==2023.3 development
pywin32-ctypes ==0.2.0 development
pyyaml ==6.0 development
rdflib ==6.2.0 development
readme-renderer ==37.3 development
requests ==2.31.0 development
requests-toolbelt ==1.0.0 development
responses ==0.23.1 development
rfc3986 ==2.0.0 development
rich ==13.4.2 development
ruamel-yaml ==0.17.21 development
ruamel-yaml-clib ==0.2.7 development
schema-salad ==8.4.20230606143604 development
scipy ==1.7.3 development
scipy ==1.10.1 development
secretstorage ==3.3.3 development
selenium ==4.10.0 development
seletools ==1.4.0 development
setuptools ==67.8.0 development
six ==1.16.0 development
sniffio ==1.3.0 development
snowballstemmer ==2.2.0 development
sortedcontainers ==2.4.0 development
sphinx ==5.3.0 development
sphinx-rtd-theme ==1.2.2 development
sphinxcontrib-applehelp ==1.0.2 development
sphinxcontrib-devhelp ==1.0.2 development
sphinxcontrib-htmlhelp ==2.0.0 development
sphinxcontrib-jquery ==4.1 development
sphinxcontrib-jsmath ==1.0.1 development
sphinxcontrib-qthelp ==1.0.3 development
sphinxcontrib-serializinghtml ==1.1.5 development
statsd ==4.0.1 development
testfixtures ==7.1.0 development
tinydb ==4.8.0 development
toml ==0.10.2 development
tomli ==2.0.1 development
trio ==0.22.0 development
trio-websocket ==0.10.3 development
tuspy ==1.0.0 development
twill ==3.1 development
twine ==4.0.2 development
typed-ast ==1.5.4 development
types-pyyaml ==6.0.12.10 development
typing-extensions ==4.6.3 development
urllib3 ==1.26.16 development
vine ==5.0.0 development
watchdog ==3.0.0 development
wcwidth ==0.2.6 development
webencodings ==0.5.1 development
werkzeug ==2.2.3 development
wrapt ==1.15.0 development
wsproto ==1.2.0 development
yarl ==1.9.2 development
zipp ==3.15.0 development

lib/galaxy/dependencies/lint-requirements.txt pypi

flake8 *
flake8-bugbear *
ruff *

lib/galaxy/dependencies/pinned-lint-requirements.txt pypi

attrs ==23.1.0
flake8 ==5.0.4
flake8-bugbear ==23.3.12
importlib-metadata ==4.2.0
mccabe ==0.7.0
pycodestyle ==2.9.1
pyflakes ==2.5.0
ruff ==0.0.272
typing_extensions ==4.6.3
zipp ==3.15.0

lib/galaxy/dependencies/pinned-requirements.txt pypi

a2wsgi ==1.7.0
adal ==1.2.7
aiobotocore ==2.4.2
aiofiles ==23.1.0
aiohttp ==3.8.4
aioitertools ==0.11.0
aiosignal ==1.3.1
alembic ==1.11.1
amqp ==5.1.1
anyio ==3.7.0
apispec ==6.3.0
appdirs ==1.4.4
arcp ==0.2.1
argcomplete ==3.1.1
async-timeout ==4.0.2
asynctest ==0.13.0
attmap ==0.13.2
attrs ==23.1.0
babel ==2.12.1
bagit ==1.8.1
bagit-profile ==1.3.1
bcrypt ==4.0.1
bdbag ==1.6.4
beaker ==1.12.1
billiard ==3.6.4.0
bioblend ==1.1.1
bleach ==6.0.0
boltons ==23.0.0
boto ==2.49.0
botocore ==1.27.59
bx-python ==0.10.0
cachecontrol ==0.13.1
cached-property ==1.5.2
celery ==5.2.7
certifi ==2023.5.7
cffi ==1.15.1
charset-normalizer ==3.1.0
cheetah3 ==3.2.6.post1
circus ==0.18.0
click ==8.1.3
click-didyoumean ==0.3.0
click-plugins ==1.1.1
click-repl ==0.3.0
cloudauthz ==0.6.0
cloudbridge ==3.1.0
colorama ==0.4.6
coloredlogs ==15.0.1
conda-package-streaming ==0.8.0
cryptography ==41.0.1
cwl-upgrader ==1.2.8
cwl-utils ==0.28
cwltool ==3.1.20221109155812
cython ==0.29.35
decorator ==5.1.1
defusedxml ==0.7.1
deprecation ==2.1.0
dictobj ==0.4
dnspython ==2.3.0
docopt ==0.6.2
docutils ==0.18.1
ecdsa ==0.18.0
edam-ontology ==1.25.2
email-validator ==2.0.0.post2
exceptiongroup ==1.1.1
fastapi ==0.97.0
fastapi-utils ==0.2.1
filelock ==3.12.2
frozenlist ==1.3.3
fs ==2.4.16
fsspec ==2023.1.0
future ==0.18.3
galaxy-sequence-utils ==1.1.5
galaxy2cwl ==0.1.4
gravity ==1.0.3
greenlet ==2.0.2
gunicorn ==20.1.0
gxformat2 ==0.18.0
h11 ==0.14.0
h5grove ==1.3.0
h5py ==3.8.0
humanfriendly ==10.0
idna ==3.4
importlib-metadata ==4.13.0
importlib-resources ==5.12.0
isa-rwval ==0.10.10
isodate ==0.6.1
jinja2 ==3.1.2
jmespath ==1.0.1
jsonref ==1.1.0
jsonschema ==4.17.3
kombu ==5.2.4
lagom ==2.4.1
lxml ==4.9.2
mako ==1.2.4
markdown ==3.4.3
markdown-it-py ==2.2.0
markupsafe ==2.1.3
mdurl ==0.1.2
mercurial ==6.4.4
mistune ==2.0.5
mrcfile ==1.4.3
msal ==1.22.0
msgpack ==1.0.5
multidict ==6.0.4
mypy-extensions ==1.0.0
networkx ==2.5
nodeenv ==1.8.0
numpy ==1.21.6
numpy ==1.24.3
numpy ==1.25.0
oauthlib ==3.2.2
orjson ==3.9.1
oyaml ==1.0
packaging ==23.1
paramiko ==3.2.0
parsley ==1.3
paste ==3.5.3
pastedeploy ==3.0.1
pebble ==5.0.3
pkgutil-resolve-name ==1.3.10
prompt-toolkit ==3.0.38
prov ==1.5.1
psutil ==5.9.5
pulsar-galaxy-lib ==0.15.2
pyasn1 ==0.5.0
pycparser ==2.21
pycryptodome ==3.18.0
pydantic ==1.10.9
pydantic-tes ==0.1.5
pydot ==1.4.2
pyeventsystem ==0.1.0
pyfaidx ==0.7.2.1
pygments ==2.15.1
pyjwt ==2.7.0
pykwalify ==1.8.0
pylibmagic ==0.4.0
pynacl ==1.5.0
pyparsing ==3.0.9
pyreadline ==2.1
pyreadline3 ==3.4.1
pyrsistent ==0.19.3
pysam ==0.21.0
python-dateutil ==2.8.2
python-jose ==3.3.0
python-magic ==0.4.27
python-multipart ==0.0.6
python3-openid ==3.2.0
pytz ==2023.3
pyyaml ==6.0
pyzmq ==25.1.0
rdflib ==6.2.0
refgenconf ==0.12.2
regex ==2023.8.8
repoze-lru ==0.7
requests ==2.31.0
requests-oauthlib ==1.3.1
requests-toolbelt ==1.0.0
requests-unixsocket ==0.3.0
rich ==13.4.2
rocrate ==0.8.0
routes ==2.5.1
rsa ==4.9
ruamel-yaml ==0.17.21
ruamel-yaml-clib ==0.2.7
s3fs ==2023.1.0
schema-salad ==8.4.20230606143604
setuptools ==67.8.0
setuptools-scm ==5.0.2
shellescape ==3.8.1
six ==1.16.0
sniffio ==1.3.0
social-auth-core ==4.0.3
sortedcontainers ==2.4.0
sqlalchemy ==1.4.48
sqlitedict ==2.1.0
sqlparse ==0.4.4
starlette ==0.27.0
starlette-context ==0.3.5
supervisor ==4.2.5
svgwrite ==1.4.3
tenacity ==8.2.2
tifffile ==2021.11.2
tinydb ==4.8.0
tornado ==6.2
tqdm ==4.65.0
tuspy ==1.0.0
tuswsgi ==0.5.5
typing-extensions ==4.6.3
tzlocal ==2.1
ubiquerg ==0.6.2
urllib3 ==1.26.16
uvicorn ==0.22.0
uvloop ==0.17.0
vine ==5.0.0
wcwidth ==0.2.6
webencodings ==0.5.1
webob ==1.8.7
whoosh ==2.7.4
wrapt ==1.15.0
yacman ==0.9.1
yarl ==1.9.2
zipp ==3.15.0
zipstream-new ==1.1.8
zstandard ==0.21.0

lib/galaxy/dependencies/pinned-typecheck-requirements.txt pypi

cffi ==1.15.1
cryptography ==41.0.1
mypy ==1.3.0
mypy-extensions ==1.0.0
pycparser ==2.21
pydantic ==1.10.9
tomli ==2.0.1
typed-ast ==1.5.4
types-Markdown ==3.4.2.9
types-PyYAML ==6.0.12.10
types-bleach ==6.0.0.3
types-boto ==2.49.18.8
types-contextvars ==2.4.7.2
types-dataclasses ==0.6.6
types-docutils ==0.20.0.1
types-paramiko ==3.2.0.0
types-pkg-resources ==0.1.3
types-python-dateutil ==2.8.19.13
types-requests ==2.31.0.1
types-six ==1.16.21.8
types-urllib3 ==1.26.25.13
typing_extensions ==4.6.3

lib/galaxy/dependencies/typecheck-requirements.txt pypi

mypy *
pydantic *
types-Markdown *
types-PyYAML *
types-bleach *
types-boto *
types-contextvars *
types-dataclasses *
types-docutils *
types-paramiko *
types-pkg-resources *
types-python-dateutil *
types-requests *
types-six *

lib/galaxy/job_execution/setup.py pypi

packages/app/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/app/pyproject.toml pypi

packages/app/test-requirements.txt pypi

mock-ssh-server * test
pkce * test
pykwalify * test
pytest * test
testfixtures * test

packages/auth/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/auth/pyproject.toml pypi

packages/auth/test-requirements.txt pypi

pytest * test

packages/config/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/config/pyproject.toml pypi

packages/config/test-requirements.txt pypi

gravity * test
pytest * test

packages/data/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/data/pyproject.toml pypi

packages/data/test-requirements.txt pypi

pytest * test

packages/files/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/files/pyproject.toml pypi

packages/files/test-requirements.txt pypi

fs-gcsfs * test
pytest * test
s3fs * test

packages/job_execution/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/job_execution/pyproject.toml pypi

packages/job_execution/test-requirements.txt pypi

pytest * test

packages/job_metrics/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/job_metrics/pyproject.toml pypi

packages/job_metrics/test-requirements.txt pypi

pytest * test

packages/meta/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/meta/pyproject.toml pypi

packages/meta/test-requirements.txt pypi

pytest * test

packages/navigation/dev-requirements.txt pypi

build * development
mypy * development
sphinx * development
twine * development

packages/navigation/pyproject.toml pypi

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